commit: 3bdd3d1c35c9e23cbc13e86dcb8c4b2321fd2620 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Fri Jul 29 20:47:12 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Fri Jul 29 20:47:12 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3bdd3d1c
sci-biology/ensembl-tools: new package, needs more fixes, upstream contacted Package-Manager: portage-2.3.0 sci-biology/ensembl-tools/ensembl-tools-85.ebuild | 47 +++++++++++++++++++++++ sci-biology/ensembl-tools/metadata.xml | 12 ++++++ 2 files changed, 59 insertions(+) diff --git a/sci-biology/ensembl-tools/ensembl-tools-85.ebuild b/sci-biology/ensembl-tools/ensembl-tools-85.ebuild new file mode 100644 index 0000000..642caf8 --- /dev/null +++ b/sci-biology/ensembl-tools/ensembl-tools-85.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module + +DESCRIPTION="Bioinformatics tools incl. Variant Effect Predictor (VEP)" +HOMEPAGE="http://grch37.ensembl.org/info/docs/tools/vep/script/index.html"; +SRC_URI="https://github.com/Ensembl/ensembl-tools/archive/release/${PV}.zip -> ${P}.zip" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="" # BUG: needs Bio::EnsEMBL::Registry +IUSE="" + +DEPEND="" +#DEPEND="dev-perl/Perl-XS +# dev-perl/Bio-DB-HTS" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/ensembl-tools-release-${PV}" + +src_install(){ + perl_set_version + insinto ${VENDOR_LIB}/${PN} + cd scripts/variant_effect_predictor || die + perl INSTALL.pl --DESTDIR="${EPREFIX}"/"${DESTDIR}" --AUTO ac + newdoc README.txt variant_effect_predictor.txt + cd ../../scripts/region_reporter || die + dobin *.pl + newdoc README.txt region_reporter.txt + cd ../../scripts/assembly_converter + dobin *.pl + insinto ${VENDOR_LIB}/${PN} + doins *.pm + newdoc README.txt assembly_converter.txt + insinto /usr/share/"${PN}"/examples + doins assemblymapper.in + cd ../../scripts/id_history_converter + dobin *.pl + newdoc README.txt id_history_converter.txt + insinto /usr/share/"${PN}"/examples + doins idmapper.in +} diff --git a/sci-biology/ensembl-tools/metadata.xml b/sci-biology/ensembl-tools/metadata.xml new file mode 100644 index 0000000..f68a1b6 --- /dev/null +++ b/sci-biology/ensembl-tools/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="person"> + <email>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata>
